Strategic Sampling of Eurasian Otter Spraints for Genetic Research in South Korea: Enhancing PCR Success and Data Accuracy
Non-invasive genetic approaches, particularly using fecal samples, are commonly used to study endangered and elusive species, as they are easy to collect with minimal permission and cause little disturbance to the subject population. However, such studies face limitations due to poor DNA yield, whic...
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MDPI AG
2025-02-01
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| Online Access: | https://www.mdpi.com/2076-2615/15/4/574 |
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| author | Jee Hyun Kim Jangmi Lee Dong Youn Kim Yoon-Do Yang Sujoo Cho Han-Chan Park Sung Yong Han Mi-Sook Min Hang Lee Je-Yoel Cho Puneet Pandey |
| author_facet | Jee Hyun Kim Jangmi Lee Dong Youn Kim Yoon-Do Yang Sujoo Cho Han-Chan Park Sung Yong Han Mi-Sook Min Hang Lee Je-Yoel Cho Puneet Pandey |
| author_sort | Jee Hyun Kim |
| collection | DOAJ |
| description | Non-invasive genetic approaches, particularly using fecal samples, are commonly used to study endangered and elusive species, as they are easy to collect with minimal permission and cause little disturbance to the subject population. However, such studies face limitations due to poor DNA yield, which affects the overall utilization of collected samples and increases data errors. Here, we evaluated the impact of sample age and collection season on the performance of DNA extracted from feces (spraints) of the Eurasian otter (<i>Lutra lutra</i>), a semi-aquatic apex predator in South Korean freshwater ecosystems. We found that PCR amplification success rates decreased more rapidly in summer (79.3–58.2%) compared to winter (99.2–84.8%) with extended environmental exposure. Genotyping error rates were higher in samples collected during summer, with the rate of error increase over time being significantly greater in summer than in winter. The hot and humid South Korean summer fosters microbial growth and fecal degradation, which negatively impacts DNA yield, reducing PCR amplification success and increasing genotyping errors. We recommend collecting otter feces during winter for better DNA quality. If sampling in summer is unavoidable, it is crucial to collect fresh samples, which can be facilitated by conducting frequent surveys of latrine sites. |
| format | Article |
| id | doaj-art-9b25a786537d4d1fbf7fac5c3c0eb428 |
| institution | DOAJ |
| issn | 2076-2615 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj-art-9b25a786537d4d1fbf7fac5c3c0eb4282025-08-20T03:11:03ZengMDPI AGAnimals2076-26152025-02-0115457410.3390/ani15040574Strategic Sampling of Eurasian Otter Spraints for Genetic Research in South Korea: Enhancing PCR Success and Data AccuracyJee Hyun Kim0Jangmi Lee1Dong Youn Kim2Yoon-Do Yang3Sujoo Cho4Han-Chan Park5Sung Yong Han6Mi-Sook Min7Hang Lee8Je-Yoel Cho9Puneet Pandey10Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of KoreaResearch Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of KoreaResearch Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of KoreaDepartment of Biological Sciences, Konkuk University, Seoul 05029, Republic of KoreaResearch Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of KoreaConservation Genome Resource Bank for Korean Wildlife, Seoul 08826, Republic of KoreaAssociation of Korean Otter Conservation, Hwacheon 24135, Republic of KoreaResearch Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of KoreaResearch Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of KoreaDepartment of Biochemistry, College of Veterinary Medicine, Research Institute for Veterinary Science, BK21 FOUR Future Veterinary Medicine Leading Education and Research Center, Seoul National University, Seoul 08826, Republic of KoreaResearch Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of KoreaNon-invasive genetic approaches, particularly using fecal samples, are commonly used to study endangered and elusive species, as they are easy to collect with minimal permission and cause little disturbance to the subject population. However, such studies face limitations due to poor DNA yield, which affects the overall utilization of collected samples and increases data errors. Here, we evaluated the impact of sample age and collection season on the performance of DNA extracted from feces (spraints) of the Eurasian otter (<i>Lutra lutra</i>), a semi-aquatic apex predator in South Korean freshwater ecosystems. We found that PCR amplification success rates decreased more rapidly in summer (79.3–58.2%) compared to winter (99.2–84.8%) with extended environmental exposure. Genotyping error rates were higher in samples collected during summer, with the rate of error increase over time being significantly greater in summer than in winter. The hot and humid South Korean summer fosters microbial growth and fecal degradation, which negatively impacts DNA yield, reducing PCR amplification success and increasing genotyping errors. We recommend collecting otter feces during winter for better DNA quality. If sampling in summer is unavoidable, it is crucial to collect fresh samples, which can be facilitated by conducting frequent surveys of latrine sites.https://www.mdpi.com/2076-2615/15/4/574non-invasive samplingEurasian otterDNA degradationPCR amplification successgenotyping errors |
| spellingShingle | Jee Hyun Kim Jangmi Lee Dong Youn Kim Yoon-Do Yang Sujoo Cho Han-Chan Park Sung Yong Han Mi-Sook Min Hang Lee Je-Yoel Cho Puneet Pandey Strategic Sampling of Eurasian Otter Spraints for Genetic Research in South Korea: Enhancing PCR Success and Data Accuracy Animals non-invasive sampling Eurasian otter DNA degradation PCR amplification success genotyping errors |
| title | Strategic Sampling of Eurasian Otter Spraints for Genetic Research in South Korea: Enhancing PCR Success and Data Accuracy |
| title_full | Strategic Sampling of Eurasian Otter Spraints for Genetic Research in South Korea: Enhancing PCR Success and Data Accuracy |
| title_fullStr | Strategic Sampling of Eurasian Otter Spraints for Genetic Research in South Korea: Enhancing PCR Success and Data Accuracy |
| title_full_unstemmed | Strategic Sampling of Eurasian Otter Spraints for Genetic Research in South Korea: Enhancing PCR Success and Data Accuracy |
| title_short | Strategic Sampling of Eurasian Otter Spraints for Genetic Research in South Korea: Enhancing PCR Success and Data Accuracy |
| title_sort | strategic sampling of eurasian otter spraints for genetic research in south korea enhancing pcr success and data accuracy |
| topic | non-invasive sampling Eurasian otter DNA degradation PCR amplification success genotyping errors |
| url | https://www.mdpi.com/2076-2615/15/4/574 |
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